After about 15 minutes, Kill was hoisted on a stretcher and rolled off the field as the crowd clapped and chanted his first name.
MarQueis Gray had another uneven performance at quarterback for the Gophers (0-2), who haven't lost their first two games to start a season since 1992, which was Jim Wacker's first year on the job.
Manley completed his first 12 passes, the last a 4-yard strike to backup tight end David Quiroga that stretched the NMSU lead to 21-7 with 6:53 left in the first half.
The Aggies set the tone from the start with a six-play, 60-yard drive. Manley hit Rogers for a 26-yard score, with cornerback Brock Vereen and safety Shady Salamon failing to reach Rogers in time.
Gray helped lead the Gophers on an 88-yard drive for a tying touchdown, a short run by Lamonte Edwards, but the majority of his throws were off the mark. McKnight made a handful of acrobatic catches, and tight end Colin McGarry dived to haul in a 10-yard score in the corner of the end zone and pull the Gophers within 21-14 right before the half.
Manley wasn't highly recruited, and head coach Dewayne Walker said he didn't have the job locked down when the season started. But he looked crisp early, completing his first 12 passes.
He made some bad throws, including two interceptions, but showed some poise and had help in the backfield from Robert Clay, who rushed 20 times for 97 yards and a touchdown. Taveon Rogers had 88 yards receiving and two scores.
Gray, who was relieved briefly in the third quarter by freshman Max Shortell, finished with 110 yards rushing on 17 attempts. He went 16 for 32 through the air for 211 yards, two touchdowns and two interceptions.
Gray threaded a perfect pass to Da'Jon McKnight on a quick post route for a 4-yard touchdown with 11:47 left, pulling the Gophers within 28-21.
He nearly tied the game later on a rollout with a head-first dive at the pylon with 7:51 left, and the initial ruling on the field was a touchdown. But a replay review determined his foot was out of bounds. On fourth and 1, Edwards was stopped and NMSU took over.
Clay and Victor Johnson ground down the clock for the Aggies, and the Gophers didn't get the ball back until 2:09 remained, starting at their own 11-yard line with no timeouts.
Gray was at his best on this final drive, but after a 13-yard scamper and a quick spike to stop the clock, Kill went down.
After the distracting delay, Gray went 0 for 3 on his last three passes and the Aggies emerged with their first win over a team from a BCS conference since beating Arizona State in 1999.